[Seth-Trips] [BABDG] June 24 meeting: Peter Schattner, UC Santa Cruz (fwd)

Praveen Sinha ampere at swcp.com
Mon Jun 14 11:30:21 PDT 2004

Just FYI, I'll be attempting to make this, in case anyone wants to tag


---------- Forwarded message ----------
Date: Sun, 13 Jun 2004 23:03:35 -0500
From: "[BABDG]" <announce at bayareabioinformatics.org>
To: ampere at swcp.com
Subject: [BABDG] June 24 meeting: Peter Schattner, UC Santa Cruz

To the Bay Area Bioinformatics Community,

Bay Area Bioinformatics is an organization open to all members of the San F=
rancisco Bay Area who have an interest in the field of Bioinformatics. The =
purposes of the organization are to represent the local community of bioinf=
ormatics professionals; to provide a monthly forum for the presentation of =
current developments in bioinformatics and other topics of interest; to pro=
mote professional and career development in bioinformatics, by encouraging =
educational programs and the dissemination of job opportunities; and to fos=
ter communication among the diverse community of professionals who work in =
bioinformatics and related fields. Please visit our web site at http://www.=

The Bay Area Bioinformatics Discussion Group is affiliated with the Interna=
tional Society for Computational Biology www.iscb.org.

We are now pleased to announce the fifty-second meeting of the Bay Area Bio=
informatics Discussion Group.


Computational Genefinding for Non-protein-coding RNAs =20

Peter Schattner
Center for Biomolecular Science and Engineering=20
UC Santa Cruz

Thursday, June 24, 2004
7:00 to 8:00 p.m. Presentation
8:00 to 9:00 p.m. Discussion and Announcements=20

Munzer Auditorium
Stanford University=20

(Unless otherwise noted, all BAB events are free of charge and require no R=
SVP or registration.)=20



Computer programs have been quite successful at detecting novel=20
protein-coding genes as well as characterizing them through their=20
similarity to previously known genes. Well known examples include=20
Genscan for gene detection and Blast for gene characterization. However,=20
these programs =96 which rely on genomic features such as long=20
open-reading-frames, codon signatures and primary sequence similarity to=20
previously known genes =96 are not useful for non-protein-coding RNA=20
(ncRNA) genes which generally do not have such features.

The first successful attempts at computational ncRNA gene-finding=20
focused on those ncRNAs for which well-characterized primary sequences=20
and/or secondary structures were available, such as transfer-RNAs=20
(tRNAs) or small nucleolar methylation-guide RNAs (snoRNAs). In addition=20
programs were developed to characterize novel ncRNAs by searching for=20
specific primary-sequence and/or secondary-structure motifs. Such=20
secondary-structure motifs might be indicated by increased Watson-Crick=20
base-pairing or by low minimum- free-energies. More recently, ncRNA=20
genefinders exploiting secondary structure conservation between ncRNAs=20
of related species have had some success in detecting ncRNAs. However,=20
in general the problem of computational detection and characterization=20
of new classes of ncRNA genes remains unsolved.

In this talk I will review the challenges involved in computational=20
ncRNA gene detection and characterization and some of the strategies=20
that have been developed to address these challenges. I will compare the=20
successes of the different approaches as well as their limitations.=20
Finally, I will consider the impact that these computational methods=20
have on our picture of the world of ncRNAs.


Speaker Background:=20

Peter Schattner is a computational biologist at the University of=20
California, Santa Cruz where his principal research interests are in=20
computer-based methods for the detection and characterization of=20
non-protein-coding RNAs. He has also been a developer for the Bioperl=20
group for whom he has designed numerous software modules and contributed=20
the project's tutorial documentation. Prior to working in computational=20
biology, he spent several years designing and developing medical imaging=20
systems (ultrasound and MRI) at Diasonics and Stanford Research=20
Institute (SRI).

Schattner received his B.A. (magna cum laude) from Swarthmore College=20
and his Ph.D. from M.I.T, both in physics. His academic and professional=20
honors include membership in Phi Beta Kappa and Sigma Xi, election as a=20
Woodrow Wilson Fellow and leadership of the research team that received=20
the 1990 Matzuk Award for Technical Innovation of the American Institute=20
of Ultrasound in Medicine. He has authored or co-authored over twenty=20
papers published in the scientific literature.


Directions to Munzer Auditorium at Stanford University:=20


Munzer Auditorium is in the Beckman Center. A map of this area of the Stanf=
ord campus is here:=20


Parking in the lot near the Beckman Center is unrestricted after 5 p.m.=20


This summer's IEEE Computational Systems Bioinformatics (CSB2004) conferenc=
e is sure to be one of the key bioinformatics events in 2004, providing a b=
road spectrum of peer-reviewed, bioinformatics-related topics covering the =
breadth and depth of this dynamically evolving field. Our topic submission =
procedures, keynote speakers, paper and poster presentations, tutorials and=
 social events have all been designed to cater to bioinformatics' eclectic =
mix of disciplines. CSB2004 also has the lowest registration fees of any co=
nference if its kind world wide, making it possible for everyone to attend.=
 However, attendance is limited by venue capacity at Stanford University so=
 please register early.

Focused tutorials take place Monday, August 16, 2004 prior to CSB2004, whic=
h begins Tuesday August 17, 2004. The purpose of the tutorial program is to=
 provide participants with relevant lectures and demonstrations on either w=
ell-established or new "cutting-edge" topics. Tutorial participants, throug=
h morning and afternoon sessions, may learn about new areas of bioinformati=
cs research, get an introduction to important established topics, and/or en=
hance already well-developed bioinformatics skills.=20

More information and early registration are currently available online at=

Current updates for CSB2004 are at: http://conferences.computer.org/bioinfo=


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